The metabolic output of a cell is the summation of the functional genomic, transcriptomic and proteomic networks that define that cell type. Metabolomics is the comprehensive and simultaneous systematic determination of metabolite levels in the metabolome and their changes over time as a consequence of stimuli. While other fields may provide information, for example, regarding the copy number of a given gene, mRNA or protein; this study of chemical processes involving metabolites provides the downstream summation of all aberrant genes, RNAs, and/or proteins. This ‘metabolic fingerprint’ represents a snapshot of all the functioning or non-functioning pathways in a particular cell type.
Several analytical methods including mass spectrometry, chromatography, and NMR spectroscopy have been used to quantify cellular metabolites. Mass spectrometry and chromatography both require small sample amounts and can be easily adapted for high throughput analysis; however, both methods typically involve at least one if not several purification steps. Furthermore, in most cases the metabolites to be examined must be pre-selected a priori. Untargeted mass spectrometry approaches are possible but require several rounds of purification and further identification methods. In addition, not all metabolites, including nucleotide analogs and lipids, are easily ionizable and thus cannot be detected via mass spectrometry. Further, the fragmentation pattern resulting from mass spectrometry is not always suitable to distinguish between molecules such as sugars that have equal mass, but different structures, hence limiting the analysis.